AIMC Topic: Transcriptome

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Spatially resolved transcriptomics and graph-based deep learning improve accuracy of routine CNS tumor diagnostics.

Nature cancer Jan 29, 2025
The diagnostic landscape of brain tumors integrates comprehensive molecular markers alongside traditional histopathological evaluation. DNA methylation and next-generation sequencing (NGS) have become a cornerstone in central nervous system (CNS) tum...
Deep Learning Humans DNA Methylation High-Throughput Nucleotide Sequencing Male Central Nervous System Neoplasms Female Biomarkers, Tumor Gene Expression Profiling Brain Neoplasms Transcriptome
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Exploring the role of oxidative stress in carotid atherosclerosis: insights from transcriptomic data and single-cell sequencing combined with machine learning.

Biology direct Jan 29, 2025
BACKGROUND: Carotid atherosclerotic plaque is the primary cause of cardiovascular and cerebrovascular diseases. It is closely related to oxidative stress and immune inflammation. This bioinformatic study was conducted to identify key oxidative stress...
Plaque, Atherosclerotic Transcriptome Carotid Artery Diseases Oxidative Stress Humans Single-Cell Analysis Machine Learning Macrophages
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Unveiling the role of PANoptosis-related genes in breast cancer: an integrated study by multi-omics analysis and machine learning algorithms.

Breast cancer research and treatment Jan 28, 2025
BACKGROUND: The heterogeneity of breast cancer (BC) necessitates the identification of novel subtypes and prognostic models to enhance patient stratification and treatment strategies. This study aims to identify novel BC subtypes based on PANoptosis-...
Transcriptome Multiomics Gene Expression Regulation, Neoplastic Algorithms Humans Machine Learning Prognosis Female Breast Neoplasms Tumor Microenvironment Biomarkers, Tumor Gene Expression Profiling
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Multimodal learning for mapping genotype-phenotype dynamics.

Nature computational science Jan 28, 2025
How complex phenotypes emerge from intricate gene expression patterns is a fundamental question in biology. Integrating high-content genotyping approaches such as single-cell RNA sequencing and advanced learning methods such as language models offers...
von Willebrand Factor Phenotype Genotype Gene Expression Profiling Genetic Association Studies Computational Biology Transcriptome Humans Single-Cell Analysis Machine Learning
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Identification of biomarkers associated with coronary artery disease and non-alcoholic fatty liver disease by bioinformatics analysis and machine learning.

Scientific reports Jan 28, 2025
The constantly emerging evidence indicates a close association between coronary artery disease (CAD) and non-alcoholic fatty liver disease (NAFLD). However, the exact mechanisms underlying their mutual relationship remain undefined. This study aims t...
Biomarkers Gene Expression Profiling Transcriptome Gene Regulatory Networks Computational Biology Humans ROC Curve Machine Learning Gene Ontology Protein Interaction Maps Databases, Genetic Coronary Artery Disease Non-alcoholic Fatty Liver Disease
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STAIG: Spatial transcriptomics analysis via image-aided graph contrastive learning for domain exploration and alignment-free integration.

Nature communications Jan 27, 2025
Spatial transcriptomics is an essential application for investigating cellular structures and interactions and requires multimodal information to precisely study spatial domains. Here, we propose STAIG, a deep-learning model that integrates gene expr...
Gene Expression Profiling Transcriptome Deep Learning Image Processing, Computer-Assisted Humans Algorithms Tumor Microenvironment
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Identification and validation of key autophagy-related genes in lupus nephritis by bioinformatics and machine learning.

PloS one Jan 27, 2025
INTRODUCTION: Lupus nephritis (LN) is one of the most frequent and serious organic manifestations of systemic lupus erythematosus (SLE). Autophagy, a new form of programmed cell death, has been implicated in a variety of renal diseases, but the relat...
Protein Interaction Maps Gene Regulatory Networks Mice Animals Gene Expression Profiling Transcriptome Autophagy Computational Biology Kidney Lupus Nephritis Machine Learning Female Humans
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Decoding cortical folding patterns in marmosets using machine learning and large language model.

NeuroImage Jan 24, 2025
Macroscale neuroimaging results have revealed significant differences in the structural and functional connectivity patterns of gyri and sulci in the primate cerebral cortex. Despite these findings, understanding these differences at the molecular le...
Machine Learning Language Animals Large Language Models Callithrix Male Transcriptome Cerebral Cortex
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Spatial transcriptome reveals histology-correlated immune signature learnt by deep learning attention mechanism on H&E-stained images for ovarian cancer prognosis.

Journal of translational medicine Jan 24, 2025
BACKGROUND: The ability to predict the prognosis of patients with ovarian cancer can greatly improve disease management. However, the knowledge on the mechanism of the prediction is limited. We sought to deconvolute the attention feature learnt by a ...
Eosine Yellowish-(YS) Hematoxylin Prognosis Female Reproducibility of Results Staining and Labeling Humans Ovarian Neoplasms Transcriptome Deep Learning
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Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.

Scientific reports Jan 24, 2025
To integrate machine learning and multiomic data on lactylation-related genes (LRGs) for molecular typing and prognosis prediction in lung adenocarcinoma (LUAD). LRG mRNA and long non-coding RNA transcriptomes, epigenetic methylation data, and somati...
Machine Learning Prognosis Female Humans Biomarkers, Tumor Mutation Lung Neoplasms Male Adenocarcinoma of Lung Gene Expression Regulation, Neoplastic Transcriptome
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